Yea, there's no need to skip Nestor (and by the same extent, Magnus in 120%). The whole thing to skip Nestor (and in general, all dragons) is only relevant to PC, as they don't use IGT, so they lose time if they don't skip it optimally.

The actual reason of why Dark Passage is faster than Sunny Flight is due to this skip existing:

This means we can get about 280 gems in this level which is significantly faster than an optimal sunny if you have fast cycles in the level despite having a slightly lower net gains over the flight. We compensated the lost gems by getting extra gems in Cliff Town and Stone Hill, which overall makes it about 2-3 seconds faster over Sunny route.

As Narwhal mentioned, if you can't hit cycles consistently, then Sunny might be faster for you. Some runners still do Sunny for that reason, in fact.

Otherwise the spreadsheet is actually nice to have, it does give some insight on the quality of the gems in each level in more detail.